As the partial government shutdown entered a record-setting fourth week, FDA Commissioner Scott Gottlieb said it was no longer “business as usual” at the agency — calling the shutdown “one of the most significant operational challenges in FDA’s recent history.”

Over the past few weeks, Gottlieb has announced multiple shifts from normal at the FDA, including that new INDs sent to the FDA won’t be considered “accepted” while the shutdown continues. Normally, INDs are considered automatically approved if the FDA doesn’t respond within 30 days. The FDA announcement stops the legal clock.

And he’s indicated that drug user fee money has been reallocated to postmarket drug safety efforts. The FDA is currently able to use carryover user fee funding from fiscal 2018 to support ongoing reviews, but Gottlieb has estimated a prolonged shutdown will exhaust the available funds, beginning with the PDUFA program, which currently has about three weeks of funding remaining.

“With no indication of a resolution to the shutdown in sight, it is likely that the effects on clinical trials and drug development programs will continue to multiply,” WCG Clinical Chief Medical Officer Lindsay McNair said last week.

“Sponsors are unsure whether they should proceed with planned screening and dosing dates at research centers; limited space at research centers may be booked far in advance, so forgoing the currently scheduled dates may mean that it takes months to get the study rescheduled,” she added.

The bigger drug sponsors seem to be in better shape at the moment than smaller companies. Spokeswomen for Novartis and GlaxoSmithKline each said that their companies’ trials haven’t yet been affected by the shutdown.

Smaller companies aren’t so sure. Biopharma company Aimmune said last week that its marketing application for a peanut allergy treatment had been thrown into limbo.

Deprived of his usual media relations team, Gottlieb has been communicating with the trials industry through his Twitter account.

When the mother of a child with a rare neurological disease said that her child’s trials had been delayed by the shutdown, Gottlieb tweeted, “Nobody should be unable to access a clinical trial or compassionate use drug owing to the funding lapse. We will help her. Our drug review staff remains at their posts across our centers.”

Since 1980, there have been at least nine government shutdowns and since the mid-1990s, they’ve grown increasingly protracted. There were two in 2018. Whether or not they directly affect trials, they’re creating a long-term uncertainty, says Michael A. Swit, a lawyer who concentrates his practice on FDA regulation.

“The lesson is, if you’re concerned about shutdowns impacting your process, make sure you get everything done in the middle of a budget cycle,” he says. “Frankly, look at everything that FDA does — the danger to the public health by the public shutdown is inexcusable.”

President Trump and Congress will take up the government funding issue again this week.